My first thought is "have you used the correct transistor?"
BDW types are typically darlington transistors with MUCH higher gain than "ordinary" transistors and that could be why the coil doesn't thump like it should? There are also many different pinouts - don't assume a replacement will have the ECB in the same order that the PCB requires.
Also, if the coil is getting hot it suggests that there is a continuous current flowing through it it? Does the replacement transistor have the same pinout as the original? This could account for both issues if the pinout is different from the PCB - coil hot AND weak knock???
Thought I would provide an update. A couple of weeks ago I desoldered the diode, then transistor. Turns out the transistor was faulty as suspected.
I replaced that and the knocker coil finally works BUT it knocks pathetically. It seems to barely make it up to knock, it sounds more like a tap than a knock. Plus the coil is getting really hot.
My next question is have I got the wrong knocker coil. I replaced the one that was in there with a brand new Gottlieb one of the same type A-1496 but I am now wondering if it's the wrong coil. A check of my Buck Rogers manual and it lists all the coils in the game except... the knocker coil. The Gottlieb manual for that era doesn't list it either. Can anyone tell me what coil should be in a system 1 knocker?
After fixing the knocker (somewhat) I noticed about 4 different switches suddenly not working so next thing will be to track that friggin problem down. 
